There was a program around here before that you could set your tileset in it and reposition so that it matched the VX's grid. Since VXAce uses the same grid(?) I'm looking for that mini-program to reposition some tiles...

Anyone know what I'm talking about?

Nope ^^
Elaborate

There's really not much more to elaborate on :/ it was about a year or two ago. You extracted the program, opened it, and selected your tilesets, Then you could drag'em onto the grid and line them up properly. It was especially useful for XP, but also good for VX and other engines.

Graphics Gale + guidelines?
Photoshop + grid?

I don't know what Graphics Gale is :\ but when I do it in Photoshop, everything's off and doesn't fit, especially windows. They're too high or too low or off-center.

What windows?

Just set up the grid to be the same size of VX tiles (Ctrl+K -> Guides, Grid & Slices -> 32 px), select the pieces you want to move and drag them with the Move tool.